You know I have a female German shepherd and the same thing happened to her. She has only had one heat so far and during it she had diarrhea too - I don't think it was total liquid like you were saying though. I remember wondering though "Is this normal?" We hadn't changed her diet and at the time we didn't have any other dogs so she didn't need to be separated or anything. So I am not sure why, if it doesn't stop within a few days I would take her to the vet. I think that the separation could have something to do with it. It probably is making her feel depresed and upset. Poor baby
But there is nothing you can really do unless you want an accidental litter! Good luck and if you get any answers that tell you anything about a connection to diarrhea and heat let me know!